#30 backfill: syntrophy/methanogenesis cohort batch 2 (9 communities)#95
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#30 backfill: syntrophy/methanogenesis cohort batch 2 (9 communities)#95realmarcin wants to merge 1 commit into
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Continues the syntrophy/methanogenesis arm of the #30 related_ingredients backfill. All entries are specific named compounds, CHEBI ids verified live via OAK, snippets verbatim from cached PMID/DOI abstracts. related_ingredients adoption: 56/265 -> 65/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Syntrophus_Methanospirillum_Gentianae_Benzoate | benzoate, dihydrogen, acetate, methane | | Thermacetogenium_Methanothermobacter_Acetate_Oxidation | acetate, dihydrogen, formate, methane | | Thermotoga_Methanocaldococcus_Hyperthermophilic | dihydrogen, carbon dioxide, methane | | Trichococcus_Syntrophomonas_Methanospirillum_Butyrate | butyrate, methane, dihydrogen, formate | | DVM_Triculture | lactate, acetate, methane, sulfate | | Geobacter_Clostridium_DIET | glycerol, propane-1,3-diol, butyrate | | Neocallimastix_Methanobrevibacter_Xylan | xylan, dihydrogen, acetate, formate | | Geobacter_Pseudomonas_Formate_Fumarate_Electroactive | formate, fumarate(2-) | | ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model | cellobiose, sulfate, fumarate(2-) | Skipped Syntrophus_Benzoate_Degrader (its one cited reference is not cached). Pre-existing CHEBI bugs flagged (out of scope): CHEBI:16775 "1,3-propanediol" is 3-aci-nitropropanoic acid (Geobacter_Clostridium_DIET); CHEBI:37686 "xylan" is alpha-D-allose (Neocallimastix); plus several acid/anion label-id mismatches (CHEBI:30746 benzoate=benzoic acid; CHEBI:30772 butyrate=butyric acid; CHEBI:18012 fumarate(2-)=fumaric acid). Added to the cleanup list. Test plan: just test (136 passed, 9 skipped), all 9 files validate clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR continues the CommunityMech related_ingredients backfill for the syntrophy/methanogenesis cohort (issue #30), adding curated CHEBI-linked ingredient entries (with evidence snippets) to nine existing community YAML records.
Changes:
- Added
related_ingredientsblocks to 9 community records to capture key substrates/products/electron carriers relevant to each community. - Included CHEBI term IDs/labels plus evidence items (PMID/DOI snippets) supporting each ingredient’s relevance.
Reviewed changes
Copilot reviewed 9 out of 9 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml | Adds butyrate/methane/H2/formate as related ingredients with PMID-backed evidence. |
| kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml | Adds H2/CO2/methane related ingredients with evidence from two publications. |
| kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml | Adds acetate/H2/formate/methane related ingredients for syntrophic acetate oxidation context. |
| kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml | Adds benzoate/H2/acetate/methane related ingredients for benzoate-degrading coculture. |
| kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml | Adds cellobiose/sulfate/fumarate related ingredients for the trophic model community. |
| kb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml | Adds xylan/H2/acetate/formate related ingredients for fungus–methanogen xylan coculture. |
| kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml | Adds formate/fumarate related ingredients for restricted-medium electroactive coculture. |
| kb/communities/Geobacter_Clostridium_DIET.yaml | Adds glycerol/1,3-propanediol/butyrate related ingredients for DIET-shifted fermentation. |
| kb/communities/DVM_Triculture.yaml | Adds lactate/acetate/methane/sulfate related ingredients for the DVM tri-culture system. |
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| - preferred_term: benzoate | ||
| chebi_term: | ||
| id: CHEBI:16150 | ||
| label: benzoate |
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| - preferred_term: fumarate | ||
| chebi_term: | ||
| id: CHEBI:29806 | ||
| label: fumarate(2-) |
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| - preferred_term: xylan | ||
| chebi_term: | ||
| id: CHEBI:37166 | ||
| label: xylan |
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| - preferred_term: 1,3-propanediol | ||
| chebi_term: | ||
| id: CHEBI:16109 | ||
| label: propane-1,3-diol | ||
| relevance: Key DIET-enhanced product; electron transfer shifts C. pasteurianum carbon | ||
| flux toward increased 1,3-propanediol, the industrially relevant target metabolite. | ||
| evidence: | ||
| - reference: PMID:28287150 | ||
| supports: SUPPORT | ||
| evidence_source: IN_VITRO | ||
| snippet: pasteurianum metabolic pattern was significantly altered towards improved | ||
| 1,3-propanediol and butyrate production (+37% and +38% resp.) | ||
| explanation: Anchors 1,3-propanediol as the metabolite increased by DIET-induced | ||
| metabolic shift. | ||
| - preferred_term: butyrate | ||
| chebi_term: | ||
| id: CHEBI:17968 | ||
| label: butyrate |
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| - preferred_term: 1,3-propanediol | ||
| chebi_term: | ||
| id: CHEBI:16109 | ||
| label: propane-1,3-diol |
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| - preferred_term: butyrate | ||
| chebi_term: | ||
| id: CHEBI:17968 | ||
| label: butyrate |
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Continues the syntrophy/methanogenesis arm of the #30
related_ingredientsbackfill (follows #94). All entries are specific named compounds; CHEBI ids verified live via OAK, snippets verbatim from cached abstracts.related_ingredientsadoption: 56/265 → 65/265.Communities (9)
Syntrophus_Benzoate_Degraderwas skipped — its one cited reference isn't cached.CHEBI:16775"1,3-propanediol" is 3-aci-nitropropanoic acid (Geobacter_Clostridium_DIET);CHEBI:37686"xylan" is alpha-D-allose (Neocallimastix); plus acid/anion label-id mismatches (CHEBI:30746benzoate=benzoic acid,CHEBI:30772butyrate=butyric acid,CHEBI:18012fumarate(2-)=fumaric acid). Added to the running cleanup list.Test plan
just test→ 136 passed, 9 skippedlinkml-validate)🤖 Generated with Claude Code